Changelog

Source: NEWS.md

rPHG 0.2.3

• Fixed issue with variable evaluation in the plotDot() function

rPHG 0.2.2

• Fixed issue with DEMO method endpoint returning incorrect dimensional data for specific Maize PHGv1 methods

rPHG 0.2.1

• Added new function, plotDot()
  • Creates dot plots from .anchorspro files
• Added new function, gvcfMetrics()
  • Creates summary metrics for a directory of gVCF files

rPHG 0.2.0

• Unified workflow for both local and server instances
• Added new class, PHGServerCon
  • New object for connecting to remote public PHG servers using BrAPI endpoints
• Added new class, PHGLocalCon
  • New object for connecting to local SQLite or PostgreSQL database instances
• Added new class, HaplotypeGraph
  • Wrapper for PHG API Java graph object
• Prior objects now use method dispatch for singular set of methods to return relevant PHG data:
  • PHGMethod()
  • showPHGMethods()
  • readSamples()
  • readRefRanges()
  • readHaplotypeIds()
  • readPHGDataSet()
• Updated summary methods:
  • numHaploPerRefRange()
  • calcMutualInfo()
  • plotGraph()
  • plotMutualInfo()

rPHG 0.1.18

• Modified availablePHGMethods():
  • Now returns only method IDs for graphs with more than 100 samples in the data
  • This prevents publicly available testing methods to be displayed for new PHG users.

rPHG 0.1.17

• Added new "DEMO" method parameter for PHGMethod() constructor:
  • specified as PHGMethod("DEMO")
  • Will download a small section (25 samples x 1000 reference ranges) of the Goodman/Buckler path data
  • Useful for testing and demonstrations

rPHG 0.1.16

• Added new function, plotGraph()
  • Returns a visNetwork object for a given section of PHG data filtered by reference range
• Updated installation information on README

rPHG 0.1.15

• Added new function, taxaByNode()
  • Returns a tibble object of taxa IDs that are found in a group of haplotype IDs for a given set of reference range IDs
• Update to latest jar files including PHG build

rPHG 0.1.14

• Update logging function (startLogger())
• Add new tests to expand code coverage
• Deprecate BrAPI calls that use external khttp client in PHG jar

rPHG 0.1.13

• Update to latest jar files including PHG build

rPHG 0.1.12

• Added BrAPI endpoint methods for obtaining PHG data from BrAPI webservices:
  • BrapiCon
  • BrapiConPHG
  • readRefRanges()
  • readSamples()
  • readTable()
  • readPHGDatasetFromBrapi()
  • filterRefRanges()
  • filterSamples()
  • serverInfo()
  • availablePHGMethods()
• Added Kotlin methods for improved data parsing speeds.
• Added new parameters in graphBuilder()
  • buildType - do you want the graph built from paths or haplotypes?

rPHG 0.1.11

• Added NEWS file for tracking version updates.
• Added error checks for catching C stack usage errors for configuration file checks in functions that require configuration file path parameters.
• Fixed edge cases in plotNumHaplo() and plotMutualInfo().